I've noticed this on the rat quest in Lower, and on the ruined staircase quest in the ruins: the catapult/ballista ammo isn't spawning in the containers, at least when I did them.

I think it may be spawning once per reset rather than once per quest.

This is exactly the case, I died to the gnomes today as our sub-par group attempted to fight them off without being able to use the siege machines. It is quite unfortunate that these machines cannot be used each time a group attempts the quest, as they can easily spell out victory for an otherwise doomed group.

-YourFriendlyNeighbourhoodDruQks

Carry your own!

were can you get it from apart from hording it from past quests?

I know of at least one place where you can buy it. I'll add others, though.